PhylomeDB: a database for genome-wide collections of gene phylogenies.

TitlePhylomeDB: a database for genome-wide collections of gene phylogenies.
Publication TypeJournal Article
Year of Publication2008
AuthorsHuerta-Cepas, J, Bueno, A, Dopazo, J, Gabaldón, T
JournalNucleic Acids Res
IssueDatabase issue
Date Published2008 Jan
KeywordsBase Sequence; Escherichia coli; Genes; Genomics; History, Ancient; Humans; Phylogeny; Proteins; Saccharomyces cerevisiae; Sequence Alignment

The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at

Alternate JournalNucleic Acids Res
PubMed ID17962297
PubMed Central IDPMC2238872